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Bathydraconidae (Notothenioidei) are a group of benthic fishes endemic to the Southern Ocean. Because of their recent evolutionary radiation and limited sampling efforts due to their occurrence in remote regions, their diversity is likely underestimated. Akarotaxis nudiceps, currently the only recognized member of its genus, is an especially poorly known bathydraconid. Although A. nudiceps has a circumpolar distribution on the Antarctic continental shelf, its deep habitat and rarity limit knowledge of its life history and biology. Using a combination of morphological and genetic analyses, we identified an undescribed species of this genus, herein named Akarotaxis gouldae sp. nov. (Banded Dragonfish). The separation of this species was initially identified from archived larval specimens, highlighting the importance of early life stage taxonomy and natural history collections. All currently known adult and larval A. gouldae sp. nov. specimens have been collected from a restricted ~400 km coastal section of the western Antarctic Peninsula, although this is possibly due to sampling bias. This region is targeted by the epipelagic Antarctic krill fishery, which could potentially capture larval fishes as bycatch. Due to the extremely low fecundity of A. gouldae sp. nov. and near-surface occurrence of larvae, we suggest the growing Antarctic krill fishery could negatively impact this speces.  

The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus’ phylogenetic position. We additionally curated E. maclovinus’ repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses. 

Abstract For any genome-based research, a robust genome assembly is required. De novo assembly strategies have evolved with changes in DNA sequencing technologies and have been through at least three phases: i) short-read only, ii) short- and long-read hybrid, and iii) long-read only assemblies. Each of the phases has their own error model. We hypothesized that hidden scaffolding errors in short-read assembly and erroneous long-read contigs degrades the quality of short- and long-read hybrid assemblies. We assembled the genome of T. borchgrevinki from data generated during each of the three phases and assessed the quality problems we encountered. We developed strategies such as k-mer-assembled region replacement, parameter optimization, and long-read sampling to address the error models. We demonstrated that a k-mer based strategy improved short-read assemblies as measured by BUSCO while mate-pair libraries introduced hidden scaffolding errors and perturbed BUSCO scores. Further, we found that although hybrid assemblies can generate higher contiguity they tend to suffer from lower quality. In addition, we found long-read only assemblies can be optimized for contiguity by sub-sampling length-restricted raw reads. Our results indicate that long-read contig assembly is the current best choice and that assemblies from phase I and phase II were of lower quality.